Biomedical subjects

Janez Demsar

Publications and source records attributed to Janez Demsar.

5 recordsLinked to original sources

PubMed2005

GenePath: from mutations to genetic networks and back.

GenePath is a web-based application for the analysis of mutant-based experiments and synthesis of genetic networks. Here, we introduce GenePath and describe a number of new approaches, including conflict resolution, handling cyclic pathways, confidence level assignment, what-if analysis and new experiment proposal. We illustrate the key concepts using data from a study of adhesion genes in Dictyostelium discoideum and show that GenePath discovered genetic interactions that were ignored in the original publication. GenePath is available at http://www.genepath.org/genepath2.

Animals↗

PubMed2005

Epistasis analysis with global transcriptional phenotypes.

Classical epistasis analysis can determine the order of function of genes in pathways using morphological, biochemical and other phenotypes. It requires knowledge of the pathway's phenotypic output and a variety of experimental expertise and so is unsuitable for genome-scale analysis. Here we used microarray profiles of mutants as phenotypes for epistasis analysis. Considering genes that regulate activity of protein kinase A in Dictyostelium, we identified known and unknown epistatic relationships and reconstructed a genetic network with microarray phenotypes alone. This work shows that microarray data can provide a uniform, quantitative tool for large-scale genetic network analysis.

Animals↗

PubMed2004

Microarray data mining with visual programming.

UNLABELLED: Visual programming offers an intuitive means of combining known analysis and visualization methods into powerful applications. The system presented here enables users who are not programmers to manage microarray and genomic data flow and to customize their analyses by combining common data analysis tools to fit their needs. AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog.

Chromosome Mapping↗

PubMed2003

GenePath: a system for automated construction of genetic networks from mutant data.

MOTIVATION: Genetic networks are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. RESULTS: We have developed GenePath, an intelligent assistant that automates the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints in the search for a plausible genetic network. GenePath formalizes genetic data analysis, facilitates the consideration of all the available data in a consistent manner, and the examination of the large number of possible consequences of planned experiments. It also provides an explanation mechanism that traces every finding to the pertinent data. AVAILABILITY: GenePath can be accessed at http://genepath.org. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://genepath.org/bi-.supp.

Animals↗

PubMedDate not supplied

GenePath: a system for inference of genetic networks and proposal of genetic experiments.

A genetic network is a formalism that is often used in biology to represent causalities and reason about biological phenomena related to genetic regulation. We present GenePath, a computer-based system that supports the inference of genetic networks from a set of genetic experiments. Implemented in Prolog, GenePath uses abductive inference to elucidate network constraints based on background knowledge and experimental results. Additionally, it can propose genetic experiments that may further refine the discovered network and establish relations between genes that could not be related based on the original experimental data. We illustrate GenePath's approach and utility on analysis of data on aggregation and sporulation of the soil amoeba Dictyostelium discoideum.

Animals↗